From b2fbe7282375b68121a32193edb40626bf1093d3 Mon Sep 17 00:00:00 2001 From: Kuoi Date: Thu, 14 Sep 2023 00:08:43 +0800 Subject: [PATCH] add: prefix --- README.md | 14 +++++++++++--- guoyi.run | 49 +++++++++++++++++++++++++++---------------------- 2 files changed, 38 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index 621128c..4719770 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv - Perform Strict consensus / Majority-rule consensus / Half strict consensus. -- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times). +- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support. - Map apomorphic characters on the consensus tree. @@ -29,13 +29,13 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv For Windows users ``` -tnt run guoyi.run filename datatype weight 0/K cons resample; +tnt run guoyi.run filename datatype weight 0/K cons resample prefix; ``` For Linux and Mac users ``` -tnt run guoyi.run filename datatype weight 0/K cons resample, +tnt run guoyi.run filename datatype weight K cons resample prefix, ``` - datatpye should be `32`, `dna`, `prot`, `num` @@ -46,6 +46,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample, - iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw) +- K is 12 (default) following Goloboff et al. 2017 (Cladistics 34: 407–437) + + - it must more than 0 + - cons should be str, mjr, hlf - mjr=majority rule, hlf=half, str=strict (default) @@ -54,6 +58,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample, - jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default) +- prefix can be empty or a string + + - default is empty + ## Results - Results instructions are at the end of `tnt.log`. diff --git a/guoyi.run b/guoyi.run index 78635e9..cffd262 100644 --- a/guoyi.run +++ b/guoyi.run @@ -1,9 +1,9 @@ -log tnt.log; - macro=; +log %7.tnt.log; + /*Arguments*/ -if ( (argnumber == 0) | (argnumber >=7) ) +if ( (argnumber == 0) | (argnumber >7) ) silent -console; quote - /----------------------------------------------------\; quote - | GUOYI TNT SCRIPT 2022-2023 MIT |; @@ -13,20 +13,25 @@ if ( (argnumber == 0) | (argnumber >=7) ) quote - | ============================== |; quote - | === Parameters Details === |; quote - | ============================== |; - quote - | filename datatype weight 0/K cons resample |; - quote - | - datatpye should be 32, dna, prot, num |; + quote - | filename type weight K cons resamp prefix |; + quote - | - type should be 32, dna, prot, num |; quote - | num=number, dna=DNA, prot=protein |; quote - | 32=max number allowed (default) |; quote - | - weight should be iw, ew, eiw |; quote - | iw=implied weight, ew=equal weight |; quote - | eiw=extended implied weight (default) |; - quote - | N.B. ew must followed 0 |; + quote - | N.B. K of ew must followed 0 (=NA) |; + quote - | - K is 12 (default) following Goloboff |; + quote - | et al. 2017 (Cladistics 34: 407–437) |; + quote - | it must more than 0 |; quote - | - cons should be str, mjr, hlf |; quote - | mjr=majority rule, hlf=half |; quote - | str=strict (default) |; - quote - | - resample should be sum of what you want |; + quote - | - resamp should be sum of what you want |; quote - | jak=1, boot=2, relative bremer=4 |; quote - | i.e. jak+boot+bremer=7 (default) |; + quote - | - prefix can be empty, or a string |; + quote - | default is empty |; quote - \----------------------------------------------------/; proc/; end @@ -181,12 +186,12 @@ else end /*Export trees*/ -export= trees.tre; +export= %7.trees.tre; taxname-; -export= trees_no.tre; +export= %7.trees_no.tre; taxname=; -tsave = trees.ctf; -tsave *= trees.tnt.tre; +tsave = %7.trees.ctf; +tsave *= %7.trees.tnt.tre; /*Consensus tree*/ if (argnumber<=4) @@ -209,11 +214,11 @@ tvault >/; /*Export consensus tree*/ tchoose /; -export - original.tre; +export - %7.original.tre; taxname-; -export - original_no.tre; -tsave = original.ctf; -tsave *= original.tnt.tre; +export - %7.original_no.tre; +tsave = %7.original.ctf; +tsave *= %7.original.tnt.tre; /*Caulculate TL/CI/RI score*/ report-; @@ -233,7 +238,7 @@ set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/ report=; /*Apomorphic characters*/ -export = winclada.tre; +export = %7.winclada.tre; taxname =; ttags=; apo >0; @@ -242,10 +247,10 @@ quote - apomorphy tags start ; ttags/; quote - apomorphy tags stop ; quote - \----------------------------------------------/; -ttags & apo.svg thickness 7 italics fontsize 15; -export < apo.tre; +ttags & %7.apo.svg thickness 7 italics fontsize 15; +export < %7.apo.tre; taxname-; -export - apo_no.tre; +export - %7.apo_no.tre; ttags-; /*Get jak/boot/relative-bremer support*/ @@ -288,15 +293,15 @@ else end /*Export consensus tree with supports*/ -ttags & resample.svg thickness 7 italics fontsize 15; +ttags & %7.resample.svg thickness 7 italics fontsize 15; quote - /----------------------------------------------\; quote - resample tags start ; ttags/; quote - resample tags stop ; quote - \----------------------------------------------/; -export < resample.tre; +export < %7.resample.tre; taxname-; -export - resample_no.tre; +export - %7.resample_no.tre; ttags-; /*Report CI/RI/TL */